Also, Affinity Publisher does not export to anything in the text based world, other than pdf - if I don't flatten the file.
When I created my ebook, I copied and pasted from the original APub doc. layout. I didn't copy and past anywhere else but into SIGIL because I thought I might get app-specific gremlins stuck to my text. Again, it's a learning curve and I'm sure my second time around will be smoother, or at least a lot more informed that I am now.
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